BN1412 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 2.3547e-05 5.3370e-04
Layer 3 3.8506e-05 1.8457e-02
Layer 2 6.7831e-05 1.8295e-02
Layer 5 1.5094e-04 8.2147e-04
Layer 6 7.4853e-04 6.1534e-03
WM 4.5066e-02 1.4974e-01
Layer 1 1.3775e-01 2.7274e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
YPEL3 Expression Distribution
Gene Specificity Score (GSS)
YPEL3 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
YPEL3 Layer 5 2.4844 0.7513
STXBP1 Layer 5 2.9922 0.7511
NDRG4 Layer 4 2.9668 0.7360
RTN3 Layer 5 2.7715 0.7349
RTN4 Layer 5 2.7012 0.7307
CLSTN1 Layer 5 2.8652 0.7307
GDI1 Layer 5 2.6895 0.7298
THY1 Layer 5 2.6719 0.7295
SYT1 Layer 5 3.2422 0.7270
DNM1 Layer 4 3.0195 0.7258
RTN1 Layer 5 2.9414 0.7241
SNRPN Layer 4 3.0449 0.7227
ENO2 Layer 5 2.8027 0.7225
CALM3 Layer 5 2.7363 0.7211
NSF Layer 5 2.6836 0.7200
EIF4A2 Layer 5 2.7793 0.7200
LMO4 Layer 4 2.5957 0.7192
AGAP3 Layer 4 2.8770 0.7178
PPP2R1A Layer 5 2.5273 0.7153
PREPL Layer 5 3.2012 0.7149
PPP3CA Layer 4 2.8516 0.7148
PKM Layer 5 2.6133 0.7148
NPTXR Layer 4 2.7246 0.7139
SYN1 Layer 5 3.2363 0.7132
KCNAB2 Layer 5 2.5693 0.7131
BSN Layer 5 2.9668 0.7130
PRNP Layer 4 2.6484 0.7119
TLE5 Layer 4 2.6426 0.7113
PNMA2 Layer 5 2.4697 0.7110
PCSK1N Layer 4 2.6719 0.7107
SNAP25 Layer 5 2.8027 0.7107
CABP1 Layer 4 2.7012 0.7097
NRGN Layer 4 2.7188 0.7088
NCDN Layer 4 2.7969 0.7083
RAB6B Layer 4 2.9277 0.7069
SERINC1 Layer 5 2.8369 0.7063
TUBA1B Layer 5 2.8965 0.7060
YWHAH Layer 5 2.6660 0.7043
UCHL1 Layer 5 2.8652 0.7038
GPX4 Layer 5 2.4082 0.7028
ARL6IP1 Layer 5 2.5781 0.7024
MAP1A Layer 5 3.0117 0.7013
BASP1 Layer 5 2.9072 0.7005
TSPYL1 Layer 5 2.9219 0.7003
VSNL1 Layer 5 3.1221 0.7002
TSPAN7 Layer 5 2.8086 0.7002
CALM1 Layer 5 2.4570 0.6997
OLFM1 Layer 2 3.0918 0.6992
NPTX1 Layer 5 2.8057 0.6989
TPI1 Layer 5 2.6543 0.6979

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1412
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1412_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1412/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1412/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1412/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1412/report/PD/BN1412_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1412/report/PD/BN1412_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 04:01:37
  • Number of Processes: 10
  • Spending Time: 0h 3m